iterate ONLY over the unmapped reads

[smangul1]

Is there a way to iterate ONLY over the unmapped reads?

Thanks,
Serghei

[AndreasHeger]

Good question, but I don't think there is, other than iterating over the complete file and filtering by 'unmapped' flag. The problem, I believe, is that unmapped reads can have a contig assigned to them, or not. Thus, unmapped reads might appear in several locations in a sorted BAM and not as a contiguous block.

[arogozhnikov]

In my case all unmapped alignments are not assigned to any contig. Still no better way than just iterate over whole file?

[bw2]

Same feature request - adding a way to iterate only over the unmapped read pairs at the end of a cram file (ie. those with ref seq id = -1 in the cram index).

[jmarshall]

Have you tried the documented way of doing this, which uses the same syntax as the underlying samtools queries:

AlignmentFile.fetch('*')

[bw2]

Wow, thanks! That's exactly what I was looking for!

The top google hits currently talk about doing this using fetch(until_eof=True)
https://pysam.readthedocs.io/en/latest/faq.html#alignmentfile-fetch-does-not-show-unmapped-reads
https://www.biostars.org/p/361215/
https://www.biostars.org/p/9542602/
etc.
but this is a much better solution.